Many years ago, a teen had been carrying a younger boy through the woods during a storm and had gotten surrounded by ninjas. He was ready to fight against overwhelming odds, but the younger boy had suddenly activated a power that brought giant roots out of the ground and had created a pillar of light.

Several years later, 14-year-old Rokujou Miharu is a boy with a very indifferent attitude living in a seaside town. One of his classmates is a boy named Aizawa Kouichi who wants to be his friend, but Miharu barely pays him any attention. The truth is that both Kouichi and their teacher Kumohira want Miharu to join the nindou (lit. way of the ninja) club.

Miharu isn’t interested though, so Kumohira comes to see him at his family okonomiyaki restaurant to inform him that he’s being targeted. Kumohira goes on to explain that he studied nindou under his grandfather and that the ninjas refer to their world as the World of Nabari, but Miharu remains uninterested and even teases Kumohira.

Meanwhile, Kouichi senses that he’s being followed and confronts his pursuer at a shrine. The pursuer turns out to be Yamase, a teacher who is also a ninja, and he wants to know if Kouichi has the hijutsu (secret art). He threatens Kouichi with a knife, but before their discussion can continue, they are interrupted by Miharu who had been drawn towards the shrine after being sent out to buy some katsuobushi for the restaurant. Yamase immediately tosses a throwing star at him, but when winds shield Miharu from danger, Yamase realizes that Miharu has the hijutsu.

Kouichi, however, manages to reach Miharu first and teleports them into the nearby forest. Unfortunately, Yamase calls his allies and has the two boys surrounded because he and his friends know that obtaining Miharu means that their chief becomes the ruler of Nabari. Miharu thus gets captured by Yamase, but shortly thereafter, a female voice in his head suggests killing everyone. This voice also promises to protect him and causes characters to appear on his skin, his eyes to glow red, and roots to sprout from the ground around him.

These roots grab Yamase’s ninja allies, but Kouichi quickly realizes the danger and reacts quickly by grabbing a sword and stabbing Miharu in the gut. As Kouichi then attempts to cast a sealing spell, the voice inside Miharu urges him to wish for something, and, and though Miharu doesn’t have a wish, his body uses a power to push Kouichi away. Kouichi is caught by Kumohira who had sensed what was going on, and Kumohira puts an end to all this by pulling the sword out of Miharu. As Miharu loses consciousness, he can hear the female voice asserting that he’ll definitely call her even though Miharu still believes that he doesn’t need anything. He wakes back up a little later in the school infirmary and is pissed off at Kouichi for what he did. When Miharu inquires about it, Kumohira explains that the hijutsu inside of him is the writing of Shinrabanshou (lit. all things in nature) which gives the ability to control all things. And even though Miharu doesn’t want it, they can’t take it out. As Kumohira and Kouichi explain that there’s one particular clan of ninjas who are after this, they sense enemies coming and prepare to fight.

Kouichi and Kumohira end up facing two ninjas apiece, however during the middle of the battle, Miharu gets captured by Yamase who brings him onto the school rooftop. Yamase roughs Miharu up a bit, but Kumohira eventually comes to save him and knocks Yamase out. In the aftermath, Miharu questions why Kouichi and Kumohira got hurt for him and wants them to stop involving themselves with him. Kumohira pays this no heed though and instead uses his own blood to mark Miharu’s forehead. He then gets on one knee and pledges himself to protect Miharu until Miharu becomes the ruler of Nabari.

Miharu, however, starts to scoot away because he remembers that he still has to go buy katsuobushi, and he tells Kumohira that he only wants to regain his indifferent life. This doesn’t discourage Kumohira, and the following day at school, he’s once again trying to convince Miharu to join the nindou club.

Okonomiyaki is a kind of omelet-style stuffed pancake. The batter is made of flour, grated yam, water or dashi (soup stock made from kelp and dried bonito flakes), eggs and shredded cabbage; other ingredients can include green onion, meat (generally pork or bacon), octopus, squid, shrimp, vegetables, kimchi (fermented cabbage), mochi (sticky rice), or cheese. "Okonomi" means "what you like" or "what you want", and "-yaki" means "grilled" or "cooked" (cf. yakitori and yakisoba); thus, the name of this dish basically means "cook whatever you like". The sharpened spatulas Miharu throws at Tobari in this episode are quite typical--they have a sharp edge since they're used to slice the okonomiyaki when it's done.